Paradox Unleashed: Mortal Men (Challenge)
by ColtKit
Summary: Yaoi AU Multi Xover, To protect the memory of sending Gallifrey away the Doctor locked away his mind. Living as John Smith, a teacher during WWII, who writes comics about an alien with powers over time. He mets a man named Jack wanting to know about the comics & the two become lovers. When the Doctor regains his memories he takes Jack on an adventure through Time & Space
1. Chapter 1

**Title:**

Paradox Unleashed series

Mortal Men

 **Summary:**

Yaoi AU Multi Xover, To protect the memory of sending Gallifrey away the Doctor locked away his mind. Living as John Smith, a teacher during WWII, who writes comics about an alien with powers over time. He mets a man named Jack wanting to know about the comics & the two become lovers. When the Doctor regains his memories he takes Jack on an adventure through Time & Space

###

 **Chapter One**

John Smith walked down the streets of Hilliard finding the quiet little town... incredibly dull. He was used to city life. He only moved out here because it was out of the way of the war. Call him a coward but he wasn't one for violence. He'd probably pass out if he even held a gun. He was a man of science, an educated man with Doctorates in physics, chemistry, engineering, and astronomy. In times of war the only place for educated men was making better bombs or teaching children. He chose the latter. He was able to get a job working at an all boys boarding school just outside of town. It came with some perks. He got his own private chambers on campus. A nice little place with two bedrooms, a bathroom, and a living room. The second bedroom he set up as his own personal workshop, he did love to tinker. The living room was covered in fully stocked bookshelves, mostly containing science fiction embarrassingly enough.

Ever since he was a child he dreamed about what was out there in the stars. He kept a dream journal and wrote down the adventures his subconscious came up with and later transformed them into comic books he would give his students. They were fairly silly but full of adventure and even educational as he made sure everything was based in science or at the very least theoretically possible. He wanted to get his students thinking and the books did a good job of that. A few months back he actually got his comics accepted by a publishing company, although he wasn't making much money off them despite them selling well. The hero of the comic, and in his dreams, was a shapeshift of sorts. So many different faces, different people from varying alien species, but at his core he was the same man. An educated man... perhaps too smart for his own good at times. He was an adventurer and explorer, a researcher and inventor. He was always a Doctor. The Doctor in his magic blue box. It was embarrassing he still dreamed of such things.

The school hired him because he was a man of science. That and their former chemistry teacher quit the day before. Apparently she won the lottery... didn't even know they had a lottery.

John was getting a reputation in the student body as the 'fun' teacher for his silly approach when it came to chemistry. John found students retain information better when you not only make it relatable but entertaining to learn. Of course Chemistry was one of the easier things to make fun with a few demonstrations. He also helped the kids with their physics homework after school, getting permission to set up a little tutoring session on any subjects the kids needed help with. It was technically John's free time so the Headmaster saw no problem if he wanted to use that to help the students. He actually seemed a little impressed John was such a dedicated teacher.

As he walked down the street John caught a few ladies staring at him and blushed, walking a bit faster and pretending he didn't notice. He was what people considered attractive but he'd always been awkward around the fairer sex... or an sex really.

John was tall and skinny with short brown hair he liked to keep spiked up for some strange reason. He had all the classic pretty boy features and dressed in expensive suits with a nice overcoat. He had with him a silver pocket watch clipped to his jacket. He didn't really know why he carried the thing around as it was broken. Bit like a secretary blanket really. He also had an old key on a silver necklace. Didn't have a clue to what the key was for either but he knew it was important... he was a little bit odd admittedly, tended to ramble. He had so many thoughts and ideas he didn't know what to do with them.

John entered one of the town pubs, the same pub he entered every day. The owner rather liked him because during an interview for his comic he mentioned this being his favorite place in the entire town. Now John didn't actually drink as he found the taste of alcohol rather vile but he did enjoy the atmosphere. They had a nice selection of typical bar games and the people were friendly. The food they served was rather good and they did sell drinks other then alcohol which John enjoyed.

As normal for this early in the day John took a seat near the window and took a stack of papers that needed grading from his suitcase. Work before pleasure of course but John felt it difficult to sit in his office all alone to grade papers. He liked the noise of crowds, which strangely helped him focus on a task. When the world was quiet and he was alone with nothing but his thought he would swear he would go mad. This place wasn't too loud but you could definitively tell people were enjoying themselves. Such a nice little place.

"Hi"

John blinked looking up from his papers to see a soldier sitting across from him at his table. The man was wearing the uniform of a United States Captain and one of those large overcoats they wore... and he was... gorgeous. This might very well be the most attractive man on the planet. He smelled just like Strawberries and something told John the man was just as tasty. John's eyes widened and he quickly shook the idea out of his head. That was NOT an appropriate thought for a teacher of all people to have about another man "Can I help you with something?"

"Oh yeah. I was hoping we could talk about this" The man pulled out one of the comic books John had written and put it on the table.

John blinked in confusion before looking at the man "No offense but aren't you a little old to be reading this? It is intended for boys 12 and under"

The man shrugged "The U.S. ships us a number of comics every now and then, mostly Captain America and Superman, but occasionally some of us buy our own over here. It's cheap entertainment"

"True" John nodded "But I'm afraid I'm a little busy at the moment, grading yesterday's homework"

"Maybe I could help with that"

John looked doubtful, no offense to the man but John worked at a luxurious private school that taught small children things most people didn't learn until university "How did you find me exactly?"

"You mentioned in your article you liked to hang out here" The man shrugged "Figured I'd swing by during shore leave and see if I could get a chance to meet you. I'm really interested in some of the ideas your comic proposed"

"Are you now?"

"Yes although I think you might have gotten it a little backwards when one of the characters said he was going to 'stabilize' a micro-petrol engine"

The Doctor blinked before smiling softly "That was supposed to be foreshadowing that the guy didn't really know what he was going. I gave my students extra credit if they caught that"

"Clever but I think outside your classroom kids are unlikely to catch that since the Doctor never explained that was what made him suspect the guy was a fraud. Might end up with a whole generation of kids thinking micro-petrol engines need to be stabilized"

The Doctor frowned putting the papers down "I can correct that in the next issue" he assured "are you talking as a concerned parent?"

"No just thought it be something that needed pointing out" The man shrugged "What does fascinate me is your books talking about 'nuclear power' so long before anyone has conceived of the idea"

"Just a theory I've been working on" John shrugged

"One of the kids in your comics was even playing an 'Xbox',"

John chuckled a bit "Yes the 'Xbox' does seem a bit ridiculous but I believe computers have the potential to advance a great deal"

"Let's cut to the chase" the man said a bit more aggressively "Where'd you meet him?"

"Who?"

"The Doctor?"

John blinked "I got the inspiration for the character based on an imaginary friend I had as a child"

The man blinked "... An imaginary friend?... Seriously?"

John scratched the back of his neck and laughed a bit "Yes I'm afraid. I would play for hours pretending I was in his magic box or on some alien world. Sometimes my friends would play with me and we'd battle our garage cans pretending they were 'Daleks'. I guess I just never grew out of that imaginative mind of a child" he shrugged picking up the comic book "Still coming up with new adventures for the Doctor, and letting a new generation of children play in his magic box"

The man blinked looking at his watch "Well thanks for the talk but I gotta run"

"I didn't catch your name"

"Jack, Captain Jack Harkness"

###

Captain Jack Harkness... was not his name. Although he had grown rather attached to it. It was the name of a soldier who died in a plane crash. It had just been convenient to take the man's identity. He was, after all, a con man. All Time Agents were to some extent but he had gone rogue. He used his training to blend into his environment and kill those who got in his way, in this case Nazis. Jack, as he did like that name, was by no means a common murderer. He just had been trained to eliminate threats, not only to the time stream. He knew how to prevent himself from becoming one. As long as he blended in and didn't do anything to big for the history books he'd be fine. His current disguise made him more of a soldier then a spy. He was a commanding officer. He already knew how to follow orders and how to give them. His role as Captain Jack Harkness was chosen because he knew how to play it, and he played it well... most of the time. There were a few cultural taboos in this century he hadn't gotten the hang of.

"W-we shouldn't" The young lieutenant blushed as Jack lightly kissed his neck.

Jack didn't really understand what the fuss was about as he'd already fucked this boy's brains out on more then one occasion. People were such prudes in this century. Sex held no deeper meaning or immoral implications in his native time period. People of the 51st century had returned to the idea of 'free love' with anyone and everyone regardless of race, creed, or species (so long as it was sentient). Sexual diseases had long since been destroyed and daily over the counter vitamins prevented them from returning in any form, as well as the pills keeping up general health.

Jack rather liked human males of this century with how bashful they could be with the added bonus that they couldn't get pregnant. A mutation occured on Earth in the early 50st century and spread to other planets via sailors, the star fairing kind. It caused males to not only produce a powerful pheromones most sentient species found appealing but also allowed them to get pregnant, although they'd need a C section to get the child out. Not all or even most humans had this gene but the ones that did tended to have a stronger libido.

Jack wasn't entirely playing fair with this boy but he couldn't really help releasing his pheromones when he was aroused and humans of this time had no defences against it. The boy was also too young and hormonal himself to put up much of a fight. Jack couldn't help thinking it was funny how the men of this century tried to put up a fight despite clearly wanting him to penetrate them.

Just as the boy moaned and Jack began unbuttoning his shirt Jack heard the sound of a cough. Looking over Jack saw General Hammer looking a mixture of disturbed, impatient, and exacerbated.

Jack had been 'discovered' by the American government and believed to be one of the alien half breeds that lived on the planet. It was easier to just go along with that then explain what was really going on so he was moved into a secret black ops department the US military. Not the most subtle cover a Time Agent should have but sometimes you need to go with what is presented.

Jack did manage to keep some future tech that was keyed to his biometrics and passed it off as the alien tech. Not like humans in this time period would know the difference. His favorite piece was the Vortex Manipulator on his wrist. He had the advanced piece of technology wrapped in leather fitting to the time period. It was a small computer on a leather band on his wrist with a strap keeping it closed. Most people paid no mind to it and those that did thought it was a watch. The Vortex Manipulator did as it's name implied. It manipulated Vortexes, the Time Vortex to be more specific. It acted as a teleportation device, instantaneously bringing him anywhere at any time in the universe. It was also a little... less then legal. He was supposed to turn his in when he left the Time Agency but instead he ran with it. It was too useful to just hand over.

The Time Agents of his era wouldn't care as the organization was just founded a few decades ago. It was still new and didn't really have the manpower to go after everyone who broke the rules on Time Travel... but then there were the Agents from the Milky Way Republic who were... less tolerant of unregistered time travellers.

They had strict rules though which bond their hands more then the cowboys of Jack's time. The Time Agency of the Milky Way Republic was very different then the ones Jack knew. They existed outside time on a base inside the Time Vortex so were unaffected by any changes to the Timeline. Time Agents were both time cops and archeologist, as well as many working civilian jobs in the star sized station hidden outside the universe... it was like a cult. The kids were taught from an early age the importance of maintaining the timeline and many become Time Agents themselves. It was like a civilization of it's own with their own laws. They were the Doctor's private army. He founded them during the time war and they continued to listen to him as their highest authority.

Agents from the Milky Way Republic were not actually allowed to use the teleportation setting on their device. They could in dire circumstances but then they had to fill out mountains of paperwork and have an investigation opened up. Stricter laws of Time Travel were past that forbid most forms of Time Travel, supposedly to prevent another Time War. Only Time Agents could legally travel through time and only through Stargates. Stargates were artificially created wormhole found on all habitable worlds of this galaxy. They were originally created to make travel between planets more convenient but were found that under the right circumstances could be used for Time Travel. In order to preserve the timeline, which meant make sure a sentient race of space ship would continue manipulating and harvesting all sentient life in the galaxy, the Stargates were commandeered and hidden on each planet were sentient life would evolve. An underground base would be built and time agents would be the only ones with access. However to insure the rise of the Goa'uld empire, and therefore humanity's later achievements, the Stargates were left alone on planets that would not one day have a sentient lifeform naturally evolve there. Other Stargates of varying models were left on Earth as well. The Goa'uld would find the Stargates as well as Earth. Although they wouldn't keep control of Earth for very long they would get plenty of humans off planet and turn them into a slave race. They would breed them and ship them out to tens of thousands of uninhabited planets. Humans would harvest resources, work in factories, and act as the host to the Goa'uld (which were large sentient parasites that needed to inhabit the body of another living thing to survive). This would continue for over five thousand years when the humans of Earth would rediscover the secrets of the Stargate and start exploring other planets. They would lead a rebellion of all the human worlds and eventually wipe out every last Goa'uld. Who cares about a little genocide now and then? A few centuries after freeing other humans however Earth would conquer most human planets and create a united government. They mostly did this to try to get a seat on the Citadel Council and to stop other species from seeing them as a 'vermin' race because of how unorganized they were and just how large their numbers were.

The Milky Way Republic's Vortex Manipulator worked with Stargates to travel to any planet at any point in time. It also had the Omnitrix functions incorporated into the design, which made it easier to blend in with alien species. Of course you couldn't forget how handy it was to transform into various alien species in a fight, particularly if the alien could shoot laser beams from it's eyes. Sadly Jack's Vortex Manipulator could do no such thing.

The General growled "You can go back to corrupting the youth with your indecent lifestyle AFTER we get to work"

"Or you could join us?" Jack grinned releasing a bit of pheromone into the room to make the man sweat.

The man stammered for a moment before he regained himself, completely ignoring Jack's comment "What can you tell me about the target?"

"Well" Jack took a seat on the chair, pulling the boy on his lap and making him sit there as he groped him in front of the general. The young man's face was bright red as he tried desperately not to look anyone in the eye "Unfortunately he's got no useful connection to the Doctor"

The General blinked "How can that be? His description of the Doctor's tools and weapons were too accurate to be coincidence"

"I said 'no useful connection' not that one doesn't exist. He was apparently a child when the Doctor abducted him. It's not like the Doctor has never done that before, although usually they are teenagers not a kid so young they believe the Doctor to be their imaginary friend"

The General eyed him "You believe that?"

"I do. I know when people are lying and this guy has no idea the Doctor is real. Must of only met him once as a very small child and picked up a few things from whatever the hell happened. However given this guy turned 'adventures with the Doctor' into a favorite childhood game it be impossible to pinpoint which adventure was real. For all we know the Doctor just materialized that box of his in the boy's room and told the kid his life story to calm him down and put him back to sleep... you know that's actually the most likely thing as the Doctor is a horrific pilot and for as irresponsible as he is I can't picture him abducting a six year old"

The General groaned "So this was a wasted trip then"

"Not quite, The Doctor tends to keep an eye on people he directly interacts with. There's a chance he might resurface. Just put a tail on the guy but don't expect anything to come of it"

"We can't exactly waste anyone right now" the General thought before looking at Jack

"Oh come on" Jack growled knowing that look.

"Out of your division your the best at infiltration with that... hormone thing you do. Get close to him and keep an eye out for the Doctor"

###

 **A/N:**

Okay first, right now Jack is Mortal and he will stay mortal throughout all of Part One of the Story. There are five parts so it's not that long by comparison. Part One will have a lot of the adventures from Season One and Two but with a spin as well as lots of original adventures, all with Jack Harkness as the main companion. This fic is largely Alternate Universe and a heavy Multi crossover with all franchises found in one universe. I recommend first reading my other fic ' **Paradox Unleashed, Chapter Zero** ' as it is a summary of the entire crossover universe in the form of a class the Doctor once sat through as a child. It explains that Time Lords accidentally pulled their planet into the Time Vortex were they evolved over the next billion years, gaining superpowers. Basically I did this to turn the Doctor into a more superhero type with powers and weaknesses and are mostly just expansions on things he's done in the show. Time Lords have enhanced physical and psychic powers. They are hard to injure but their enhanced senses make them feel pain more intensely through their sense of touch. This was kind of true in the show seeing all the things the Doctor has survived and didn't need to regenerate from. Even if it doesn't leave a bruise punches still hurt and disorient them. If something does break their skin they can become overwhelmed by pain and as their bodies evolved to prevent external injury any foreign object in the body can be lethal. Most guns only bruise but armor piercing can kill. They are far stronger, faster, and more agile then most alien species. The Doctor knows a type of Time Lord marital art that does mental attacks with physical contact using quick strikes. Their enhanced psychic abilities gives Time Lords better telepathic abilities, although the Doctor rather sucks at it compared to his people in most cases but his mental shields are far superior, as well as telekinesis which can be used to move nearby objects or on himself for flight if focus is maintained. Their ability to regenerate has also been enhanced due to the Time Vortex. Whenever their body dies it can restructure itself into any lifeform in the universe. Most of my AU version of Doctor Who has him regenerating into aliens instead of the Classic Doctors, only one I kept was the 4th. I did this because I never watched Classic Who and I am not only not attached to those characters but could not represent them properly. I have, however, seen enough of the 4th Doctor that I I believe I can capture his personality. I didn't keep the Christopher Eccleston 9th Doctor regeneration either. Instead the Doctor goes straight from being the War Doctor to the 10th. Time Lords abilities have also extended from seeing time to being able to control the individual timestreams of people, objects, or small areas but not time as a whole. They have an extra organ which stores up energy from the Time Vortex that allows them to do this. Once that energy is depleted they can only continue using this power through accessing their regeneration energy which cost them years of life their body has. The Vortex Energy does slowly restrores itself but it can take an hour or so. they can't use this power in a fixed point because the timestream isn't flexible enough to manipulate.


	2. Challenge

I'm sorry to say that I won't be continuing this story instead anyone who is interested can take it up. Consider this a Challenge. If you like the story run with it. See where you can take it.

I have way to many story and I'm always coming up with more. Honestly I'm more interested in my Midgard series

From now on this is what I'm going to do. I will declare the story as a challenge in the first chapter then, since I get hundreds of ideas for stories, what I'll do is write out the first chapter as an example of the challenge. Anyone and everyone interested can go with it.


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